Thank you so much for your very detailed answer! I think, I'll go with solution 2 and try modifying our converter such that it outputs the blocks to separate files. Or rather, in a first attempt, I will simply discard blocks 2 through 5 completely, since I don't really need this information right now anyway.
Best regards, Oliver On 07/10/10 08:52, Biddiscombe, John A. wrote: > Oliver, > > I received your files (off list) and gave them a try. I see now what the > problem is. > > You've got a temporal collection, and inside this, is a multi-block set of > particles. What is happening is that the pathline filter is being called once > per block by the executive, but the DATA_TIME_STEPS key is stamped on the > multi-block wrapper, and each time the pathline filter is executed on a > sub-block, the sub-block is extracted from the collection and passed in - > without - the DATA_TIME_STEPS key stamped on it. > > Now this is fixable in two ways. > 1) Have the executive stamp the sub-blocks with the wrapper's TIME key as > they are extracted and passed in. > 2) Have the Xdmf reader stamp the sub-blocks as they are generated (easier to > do IMHO). > > BUT. > > Even if we make one of these fixes, I suspect the pathline filter will fail. > This is because the pathline filter caches particle positions (w.r.t time) > each time it is executed and builds a trail for each particle ID. If it is > looped over a multiblock dataset - the executive reuses the same copy of the > pathline filter for each block - so the pathline filter will get highly > confused as it receives 5 executions for each time step - and the ID's > present will be also occur 5 times (assuming you have Ids from 0-N for each > block, if you have 0-5N and they are not duplicated, then it might just be > OK). > > Anyway. This is a serious problem as the pathline filter won't operate on the > multiblock data. I'll add this to my list of 'one day I must fix this' - > actually, I will soon need to use the pathline filter on multiblock data > myself, so this is a good heads-up that I need to do something. > > Here are ideas - > > Solution 1: Doesn't work. If you use Extract-Block filter in ParaView, it > just creates a new multiblock dataset with the unwanted blocks removed - it > doesn't solve the problem of the sub-block stamping, you'd still need to fix > 2) above in the reader. I have my own vtkFlattenDataset Filter (similar to > extract blocks but removes the multiblock hierarchy) which I tried and it > does work (for one block, but I didn't check for multiple to see if Ids are > reused across blocks as my filter appends the datasets if >1 are taken). > Unfortunately, this filter is not very well tested so not safe for public > consumption. > > Solution 2: If you can you split your blocks into separate Xdmf files so that > you load 5 files instead of 1 (sorry, this is painful), then all will be ok. > _This will at least work_ > > Solution 3: I could add multiblock support for the pathline filter, but this > would take a spare afternoon/day which I don't have right now. > > If I think of a solution 4, I'll post again. > > JB > > > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Biddiscombe, John A. > Sent: 06 October 2010 15:30 > To: Oliver Fochler; [email protected] > Subject: Re: [Paraview] Particle trajectories with Paraview - How to to use > an existing dataset (xml / hdf5) - error messages with "Particle Pathlines" > > Oliver > > The Xdmf file (or reader) must be not handling the time properly, can you > send (or ftp if big) me xdmf and hdf files and I'll have a look at it. I use > the pathline filter extensively and know it works ok. > > JB > > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Oliver Fochler > Sent: 06 October 2010 14:36 > To: [email protected] > Subject: [Paraview] Particle trajectories with Paraview - How to to use an > existing dataset (xml / hdf5) - error messages with "Particle Pathlines" > > Dear Paraview users, > > I know that this topic has probably been discussed a couple of times. > But so far I haven't been able to get find any real solutions from the > discussion threads to my specific problem. I'm afraid I will need a > detailed dummy / newbie explanation.. > > > What I would like to do: > ---------------------------------------- > > Plot the trajectory of a moving particle, i.e. trace its path with some > sort of line. The position of the particle is given as x,y,z coordinates > (euclidean position) at certain distinct time steps. > The ability to fade out the track after n time steps would be nice. And > of course I need more than one particle, but that doesn't really matter. > > > The data format I have: > ---------------------------------------- > > I'm using a converter written by someone else to convert the output of > my simulations to a format that is understood by paraview. In principle > I do have the source code of this converter, but I haven't really > bothered to look into it yet (and don't really have the time to do so now). > The output I get from this converter is hdf5, i.e. a xml file and a .h5 > file. The data is organized in frames, one frame per time step. See > below for an excerpt from my xml file. > > In principle this dataset just holds the positions and momenta of point > like particles (plus some more scalar values) at given time steps. > > > > What I've done so far / Error messages: > -------------------------------------- > > Loading this dataset (the xml file) into paraview works fine. It > displays all the points and animating is no problem. Each frame is > correctly associated with the actual time (as denoted in the xml file) > and I can loop through the time steps to see the particles evolve, > inspect scalar properties with glyphs and so on. > > But how can I get the trajectory of a particle? Or rather the polyline > connecting the coordinate points the particle has passed at the given > time steps. > > I've tried using the "Particle Pathlines" filter but it gives me error > messages like > > "vtkCompositeDataPipeline (0x5c93630): Algorithm > vtkTemporalPathLineFilter(0x54ff590) returned failure for request: > vtkInformation (0x55b9160)" > > for Paraview 3.6.2 or > > "vtkTemporalPathLineFilter (0x4b7a680): The input dataset did not have a > valid DATA_TIME_STEPS information key" > and > "vtkCompositeDataPipeline (0x4b7c0c0): Algorithm > vtkTemporalPathLineFilter(0x4b7a680) returned failure for request: > vtkInformation" > > for Paraview 3.8.0 > > > > > I would be very glad if you had some suggestions! > > Cheers, > Oliver > > > > Here's the beginning of my xml file: > > > <?xml version="1.0" ?> > <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []> > <Xdmf xmlns:xi="http://www.w3.org/2003/XInclude"; Version="2.2" > Name="Case: BAMPS_test"> > <Domain Name="myDomain"> > <Grid Name="euclidean position" GridType="Collection" > CollectionType="Unset"> > <Grid Name="Event 1" GridType="Collection" CollectionType="Temporal"> > <Grid Name="Frame 1" GridType="Uniform"> > <Topology Name="Topology" TopologyType="Polyvertex" > Dimensions="1019"/> > <Geometry Name="Geometry" GeometryType="XYZ"> > <DataItem NumberType="Float" Precision="4" Dimensions="1019 > 3" Format="HDF">BAMPS_test.h5:/Case/Event 1/Frame 1/euclidean > position</DataItem> > </Geometry> > <Time TimeType="Single" Value="0.2"/> > <Attribute Name="azimuthal angle" AttributeType="Scalar" > Center="Node"> > <DataItem NumberType="Float" Precision="4" Dimensions="1019" > Format="HDF">BAMPS_test.h5:/Case/Event 1/Frame 1/azimuthal angle</DataItem> > </Attribute> > <Attribute Name="electric charge" AttributeType="Scalar" > Center="Node"> > <DataItem NumberType="Float" Precision="4" Dimensions="1019" > Format="HDF">BAMPS_test.h5:/Case/Event 1/Frame 1/electric charge</DataItem> > </Attribute> > <Attribute Name="energy" AttributeType="Scalar" Center="Node"> > <DataItem NumberType="Float" Precision="4" Dimensions="1019" > Format="HDF">BAMPS_test.h5:/Case/Event 1/Frame 1/energy</DataItem> > </Attribute> > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Please keep messages on-topic and check the ParaView Wiki at: > http://paraview.org/Wiki/ParaView > > Follow this link to subscribe/unsubscribe: > http://www.paraview.org/mailman/listinfo/paraview > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Please keep messages on-topic and check the ParaView Wiki at: > http://paraview.org/Wiki/ParaView > > Follow this link to subscribe/unsubscribe: > http://www.paraview.org/mailman/listinfo/paraview > > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
